BN1862 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 4.9512e-08 9.5991e-04
Layer 4 1.0176e-06 2.9456e-04
Layer 6 1.3437e-06 1.9446e-03
Layer 5 7.2195e-06 2.3717e-04
WM 9.5591e-04 1.6610e-01
Layer 2 2.8099e-03 4.8671e-01
Layer 1 7.1180e-01 5.8632e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
DCTN1 Expression Distribution
Gene Specificity Score (GSS)
DCTN1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
DCTN1 Layer 5 2.1348 0.7379
CEND1 Layer 5 2.4238 0.7375
ATP13A2 Layer 5 2.2832 0.7335
FEM1B Layer 4 2.3809 0.7308
EPDR1 Layer 5 2.3027 0.7237
UBE2N Layer 4 2.2832 0.7234
ELAVL4 Layer 5 2.6191 0.7214
SLC6A17 Layer 4 2.6777 0.7187
CLVS2 Layer 5 2.1348 0.7179
HK1 Layer 5 2.4727 0.7175
SORL1 Layer 4 2.3340 0.7167
DNAJC5 Layer 5 2.2832 0.7167
GRINA Layer 5 2.2969 0.7138
IQSEC1 Layer 5 2.4785 0.7128
EFR3A Layer 4 2.3496 0.7121
NCOA7 Layer 5 2.2363 0.7119
GABBR1 Layer 5 2.2773 0.7117
NBL1 Layer 5 2.2715 0.7108
MORF4L2 Layer 4 2.1914 0.7098
NCALD Layer 6 2.5449 0.7098
UQCRC1 Layer 4 2.2266 0.7092
RASGRF1 Layer 5 2.3398 0.7091
KIAA0513 Layer 4 2.4082 0.7089
RAP1GAP Layer 5 2.3711 0.7089
INPP5F Layer 5 2.4336 0.7082
PTEN Layer 5 2.2773 0.7059
EVL Layer 5 2.3867 0.7059
PIP4K2B Layer 4 2.1777 0.7057
RAB6A Layer 5 2.2129 0.7045
NDRG3 Layer 4 2.2676 0.7044
CAMK2D Layer 5 2.7539 0.7043
SEZ6L2 Layer 5 2.2715 0.7040
ZYG11B Layer 5 2.3809 0.7037
ENTPD6 Layer 5 2.4238 0.7037
TTC9B Layer 5 2.7715 0.7033
NDUFV2 Layer 5 2.2578 0.7031
LARP1 Layer 4 2.2676 0.7031
CCDC85B Layer 6 2.2324 0.7030
CYC1 Layer 5 2.2461 0.7028
RCN2 Layer 5 2.2363 0.7026
MAGED1 Layer 5 2.3496 0.7018
ATL1 Layer 5 2.3242 0.7016
MAPK9 Layer 5 2.3965 0.7015
TUBB Layer 5 2.1914 0.7014
ATP9A Layer 4 2.2070 0.7013
UBE2M Layer 5 2.2227 0.7013
APBA2 Layer 5 2.1777 0.7013
SYNJ1 Layer 5 2.4395 0.7012
SYNGR1 Layer 5 2.5332 0.7010
OAT Layer 4 2.2168 0.7005

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1862
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1862_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1862/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1862/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1862/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1862/report/PD/BN1862_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1862/report/PD/BN1862_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 08:59:01
  • Number of Processes: 10
  • Spending Time: 0h 3m